Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 814/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicDistributions 1.15.0 (landing page) Kristyna Kupkova
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicDistributions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GenomicDistributions |
Version: 1.15.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GenomicDistributions_1.15.0.tar.gz |
StartedAt: 2024-11-22 01:31:47 -0500 (Fri, 22 Nov 2024) |
EndedAt: 2024-11-22 01:34:59 -0500 (Fri, 22 Nov 2024) |
EllapsedTime: 192.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicDistributions.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GenomicDistributions_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GenomicDistributions.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GenomicDistributions/DESCRIPTION' ... OK * this is package 'GenomicDistributions' version '1.15.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'GenomicDistributions' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getGeneModelsFromGTF 8.56 0.51 9.07 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
GenomicDistributions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GenomicDistributions ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GenomicDistributions' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicDistributions)
GenomicDistributions.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library("GenomicDistributions") Loading required package: IRanges Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: GenomeInfoDb > > test_check("GenomicDistributions") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_all.R:139:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ] > > proc.time() user system elapsed 28.68 1.73 30.45
GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings
name | user | system | elapsed | |
binBSGenome | 0 | 0 | 0 | |
binChroms | 0.02 | 0.00 | 0.01 | |
binRegion | 0 | 0 | 0 | |
calcChromBins | 2.40 | 0.02 | 2.42 | |
calcChromBinsRef | 0.00 | 0.02 | 0.03 | |
calcChromBinsRefSlow | 0.00 | 0.01 | 0.02 | |
calcCumulativePartitions | 2.33 | 0.11 | 2.43 | |
calcCumulativePartitionsRef | 1.63 | 0.06 | 1.69 | |
calcDinuclFreq | 0 | 0 | 0 | |
calcDinuclFreqRef | 0 | 0 | 0 | |
calcExpectedPartitions | 2.01 | 0.14 | 2.15 | |
calcExpectedPartitionsRef | 2.44 | 0.09 | 2.53 | |
calcFeatureDist | 0.14 | 0.02 | 0.16 | |
calcFeatureDistRefTSS | 0.24 | 0.00 | 0.23 | |
calcGCContent | 0 | 0 | 0 | |
calcGCContentRef | 0 | 0 | 0 | |
calcNearestNeighbors | 0.06 | 0.00 | 0.06 | |
calcNeighborDist | 0.03 | 0.00 | 0.03 | |
calcPartitions | 1.78 | 0.16 | 1.94 | |
calcPartitionsRef | 1.97 | 0.12 | 2.09 | |
calcSummarySignal | 0.05 | 0.00 | 0.05 | |
calcWidth | 0 | 0 | 0 | |
dot-validateInputs | 0 | 0 | 0 | |
dtToGr | 0.01 | 0.00 | 0.01 | |
genomePartitionList | 2.14 | 0.06 | 2.21 | |
getChromSizes | 0.02 | 0.00 | 0.01 | |
getChromSizesFromFasta | 0.00 | 0.02 | 0.02 | |
getGeneModels | 0.06 | 0.03 | 0.09 | |
getGeneModelsFromGTF | 8.56 | 0.51 | 9.07 | |
getGenomeBins | 1.30 | 0.03 | 1.33 | |
getTssFromGTF | 0.15 | 0.02 | 0.17 | |
loadBSgenome | 0 | 0 | 0 | |
loadEnsDb | 0 | 0 | 0 | |
nlist | 0 | 0 | 0 | |
plotChromBins | 0.07 | 0.00 | 0.06 | |
plotCumulativePartitions | 3.46 | 0.06 | 3.53 | |
plotDinuclFreq | 0.02 | 0.02 | 0.04 | |
plotExpectedPartitions | 1.77 | 0.09 | 1.85 | |
plotFeatureDist | 0.34 | 0.00 | 0.35 | |
plotGCContent | 0.05 | 0.00 | 0.05 | |
plotNeighborDist | 0.03 | 0.00 | 0.03 | |
plotPartitions | 2.11 | 0.00 | 2.11 | |
plotQTHist | 0.03 | 0.00 | 0.03 | |
plotSummarySignal | 0.11 | 0.00 | 0.11 | |
retrieveFile | 0 | 0 | 0 | |